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generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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-\name{anno_oncoprint_barplot}
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-\alias{anno_oncoprint_barplot}
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-\title{
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-Barplot Annotation for oncoPrint
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-}
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-\description{
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-Barplot Annotation for oncoPrint
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-}
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-\usage{
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-anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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-    bar_width = 0.6, ylim = NULL, axis = TRUE,
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-    axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
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-    width = NULL, height = NULL, border = FALSE)
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-}
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-\arguments{
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-
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-  \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
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-  \item{which}{Is it a row annotation or a column annotation?}
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-  \item{bar_width}{Width of the bars.}
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-  \item{ylim}{Data range.}
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-  \item{axis}{Whether draw axis?}
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-  \item{axis_param}{Parameters for controlling axis.}
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-  \item{width}{Width of the annotation.}
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-  \item{height}{Height of the annotation.}
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-  \item{border}{Whether draw the border?}
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-
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-}
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-\details{
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-This annotation function should always be used with \code{\link{oncoPrint}}.
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-}
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-\author{
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-Zuguang Gu <z.gu@dkfz.de>
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-}
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-\examples{
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-# There is no example
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-NULL
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-
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-}
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
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@@ -34,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
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@@ -34,5 +34,4 @@ Zuguang Gu <z.gu@dkfz.de>
34 34
 \examples{
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 # There is no example
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 NULL
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-
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 }
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add ylim in anno_oncoprint_barplot()

Zuguang Gu authored on 10/06/2019 16:20:21
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@@ -8,7 +8,7 @@ Barplot Annotation for oncoPrint
8 8
 }
9 9
 \usage{
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 anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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-    bar_width = 0.6, axis = TRUE,
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+    bar_width = 0.6, ylim = NULL, axis = TRUE,
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     axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
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     width = NULL, height = NULL, border = FALSE)
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 }
... ...
@@ -17,9 +17,10 @@ anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
17 17
   \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
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   \item{which}{Is it a row annotation or a column annotation?}
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   \item{bar_width}{Width of the bars.}
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+  \item{ylim}{Data range.}
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   \item{axis}{Whether draw axis?}
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   \item{axis_param}{Parameters for controlling axis.}
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-  \item{width}{Wisth of the annotation.}
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+  \item{width}{Width of the annotation.}
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   \item{height}{Height of the annotation.}
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   \item{border}{Whether draw the border?}
25 26
 
Browse code

set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
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@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
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 # There is no example
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 NULL
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+
36 37
 }
Browse code

add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
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@@ -33,5 +33,4 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

update

Zuguang Gu authored on 30/10/2018 08:58:14
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@@ -7,17 +7,21 @@ Barplot Annotation for oncoPrint
7 7
 Barplot Annotation for oncoPrint
8 8
 }
9 9
 \usage{
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-anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
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-    width = NULL, height = NULL, border = FALSE, ...)
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+anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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+    bar_width = 0.6, axis = TRUE,
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+    axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
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+    width = NULL, height = NULL, border = FALSE)
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 }
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 \arguments{
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   \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
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   \item{which}{Is it a row annotation or a column annotation?}
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+  \item{bar_width}{Width of the bars.}
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+  \item{axis}{Whether draw axis?}
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+  \item{axis_param}{Parameters for controlling axis.}
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   \item{width}{Wisth of the annotation.}
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   \item{height}{Height of the annotation.}
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   \item{border}{Whether draw the border?}
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-  \item{...}{Other parameters passed to \code{\link{anno_barplot}}.}
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 }
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 \details{
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
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@@ -1,10 +1,10 @@
1 1
 \name{anno_oncoprint_barplot}
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 \alias{anno_oncoprint_barplot}
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 \title{
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-Barplot annotation for oncoPrint
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+Barplot Annotation for oncoPrint
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 }
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 \description{
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-Barplot annotation for oncoPrint
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+Barplot Annotation for oncoPrint
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 }
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 \usage{
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 anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
... ...
@@ -12,8 +12,8 @@ anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
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 }
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 \arguments{
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-  \item{type}{A vector of the alteration types in your data. It can be a subset of all alteration types if you don't want to show them all.}
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-  \item{which}{Is ti a row annotation or a column annotation?}
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+  \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
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+  \item{which}{Is it a row annotation or a column annotation?}
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   \item{width}{Wisth of the annotation.}
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   \item{height}{Height of the annotation.}
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   \item{border}{Whether draw the border?}
... ...
@@ -21,7 +21,7 @@ anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
21 21
 
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 }
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 \details{
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-This annotation function should always use with \code{\link{oncoPrint}}.
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+This annotation function should always be used with \code{\link{oncoPrint}}.
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 }
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

update

Zuguang Gu authored on 17/10/2018 06:09:36
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@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
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@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
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@@ -12,13 +12,16 @@ anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
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 }
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 \arguments{
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-  \item{type}{-type}
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-  \item{which}{-which}
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-  \item{width}{-width}
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-  \item{height}{-height}
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-  \item{border}{-border}
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-  \item{...}{-...}
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+  \item{type}{A vector of the alteration types in your data. It can be a subset of all alteration types if you don't want to show them all.}
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+  \item{which}{Is ti a row annotation or a column annotation?}
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+  \item{width}{Wisth of the annotation.}
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+  \item{height}{Height of the annotation.}
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+  \item{border}{Whether draw the border?}
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+  \item{...}{Other parameters passed to \code{\link{anno_barplot}}.}
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+}
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+\details{
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+This annotation function should always use with \code{\link{oncoPrint}}.
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 }
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
... ...
@@ -26,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
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@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
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@@ -1,16 +1,24 @@
1 1
 \name{anno_oncoprint_barplot}
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 \alias{anno_oncoprint_barplot}
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 \title{
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-Column barplot annotation for oncoPrint
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+Barplot annotation for oncoPrint
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 }
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 \description{
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-Column barplot annotation for oncoPrint
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+Barplot annotation for oncoPrint
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 }
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 \usage{
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-anno_oncoprint_barplot()
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+anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
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+    width = NULL, height = NULL, border = FALSE, ...)
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 }
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-\details{
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-This function is only used for column annotation
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+\arguments{
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+
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+  \item{type}{-type}
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+  \item{which}{-which}
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+  \item{width}{-width}
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+  \item{height}{-height}
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+  \item{border}{-border}
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+  \item{...}{-...}
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+
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 }
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 \author{
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 Zuguang Gu <z.gu@dkfz.de>
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@@ -18,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>
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 \examples{
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 # There is no example
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 NULL
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-
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 }
Browse code

merge by copy paste

Zuguang Gu authored on 17/10/2017 20:55:32
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@@ -1,17 +1,10 @@
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 \name{anno_oncoprint_barplot}
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 \alias{anno_oncoprint_barplot}
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 \title{
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-<<<<<<< HEAD
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 Column barplot annotation for oncoPrint
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 }
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 \description{
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 Column barplot annotation for oncoPrint
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-=======
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-Column barplot annotaiton for oncoPrint
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-}
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-\description{
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-Column barplot annotaiton for oncoPrint
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->>>>>>> bioc/master
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 }
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 \usage{
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 anno_oncoprint_barplot()
Zuguang Gu authored on 17/10/2017 19:44:53
Showing0 changed files
Browse code

fix typo

Zuguang Gu authored on 20/08/2017 05:56:30
Showing1 changed files
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@@ -1,10 +1,10 @@
1 1
 \name{anno_oncoprint_barplot}
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 \alias{anno_oncoprint_barplot}
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 \title{
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-Column barplot annotaiton for oncoPrint
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+Column barplot annotation for oncoPrint
5 5
 }
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 \description{
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-Column barplot annotaiton for oncoPrint
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+Column barplot annotation for oncoPrint
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 }
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 \usage{
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 anno_oncoprint_barplot()
Browse code

resove conflict

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@120116 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 14/08/2016 09:20:57
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new file mode 100644
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@@ -0,0 +1,22 @@
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+\name{anno_oncoprint_barplot}
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+\alias{anno_oncoprint_barplot}
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+\title{
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+Column barplot annotaiton for oncoPrint
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+}
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+\description{
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+Column barplot annotaiton for oncoPrint
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+}
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+\usage{
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+anno_oncoprint_barplot()
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+}
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+\details{
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+This function is only used for column annotation
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+}
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+\author{
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+Zuguang Gu <z.gu@dkfz.de>
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+}
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+\examples{
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+# There is no example
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+NULL
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+
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+}
Browse code

removed 'min_gene' in 'oncoPrint()'

Zuguang Gu authored on 03/08/2016 19:36:59
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@@ -18,4 +18,5 @@ Zuguang Gu <z.gu@dkfz.de>
18 18
 \examples{
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 # There is no example
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 NULL
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+
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 }
Browse code

export anno_oncoprint_barplot()

Zuguang Gu authored on 30/06/2016 08:06:47
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new file mode 100644
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@@ -0,0 +1,21 @@
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+\name{anno_oncoprint_barplot}
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+\alias{anno_oncoprint_barplot}
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+\title{
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+Column barplot annotaiton for oncoPrint
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+}
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+\description{
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+Column barplot annotaiton for oncoPrint
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+}
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+\usage{
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+anno_oncoprint_barplot()
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+}
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+\details{
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+This function is only used for column annotation
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+}
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+\author{
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+Zuguang Gu <z.gu@dkfz.de>
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+}
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+\examples{
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+# There is no example
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+NULL
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+}